I've also seen this and couldn't figure out what was going on. It doesn't make sense because you would expect the opposite effect (you would expect a decrease in absorbance from re-oxidation of the DTNB).

I've found the best way to quantitate thiols with DTNB is to include a standard for comparison where the number of thiols are know. You can use freshly made dithiothreitol (DTT), make a standard curve and compare to your thiolated DNA. It should eliminate the slow change over time issue.